The rule was passed in November by China's southern island province of Hainan and took effect this year as tensions have escalated over overlapping claims to the waters between China, the Philippines, Vietnam and other nations.
Gazmin, visiting a military camp in the northern Philippines, said the Hainan law did not apply to Philippine territorial waters, some of which overlap with those of China which claims most of the South China Sea.
"We still have the capability to secure them (Filipino fishermen)," Gazmin said.
The Philippines has been locked in an increasingly tense standoff with China involving disputed reefs and islands in the South China Sea, in an area Manila calls the West Philippine Sea.
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Gazmin said the Philippine government would provide escort vessels to Filipino fishermen "if necessary".
The Philippine foreign department on Tuesday alleged that the Hainan rule impinges on the Philippines' exclusive economic zone, an area extending 200 miles from its coast where it has sovereign rights to explore and exploit the natural resources under a UN convention ratified in 1982.
The Chinese eventually gained control of the outcrop after Manila backed down. However, the government sought UN arbitration to settle the dispute, a move rejected by China.
"China has been projecting herself as a superpower, but chooses to pick on small countries like ours that have puny military capability," Gazmin said Thursday.
He cited the Hainan fishing rule as well as Beijing's earlier unilateral declaration of an air defence zone over the East China Sea that includes areas disputed with Japan.